RNAP II processivity is a limiting step for HIV-1 transcription independent of orientation to and activity of endogenous neighboring promoters

Virology

Volumn 486, Issue , 2015, Pages 7-14

  Kaczmarek Michaels, Katarzyna ^a   Wolschendorf, Frank ^b   Schiralli Lester, Gillian M ^c   Natarajan, Malini ^d   Kutsch, Olaf ^b   Henderson, Andrew J ^a  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University of Alabama at Birmingham   (United States)

^c UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^d STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

Author keywords

HIV latency; NELF; RNA Polymerase II pausing; Transcription interference

Indexed keywords

RNA POLYMERASE II; NELF PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE EXPRESSION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROVIRUS; VIRUS CHARACTERIZATION; VIRUS DNA CELL DNA INTERACTION; VIRUS EXPRESSION; VIRUS INDUCTION; VIRUS INHIBITION; VIRUS LATENCY; VIRUS REACTIVATION; VIRUS TRANSCRIPTION; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METABOLISM; PHYSIOLOGY; VIROLOGY;

GENE EXPRESSION REGULATION, VIRAL; HIV INFECTIONS; HIV-1; HOST-PATHOGEN INTERACTIONS; HUMANS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84942015325     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2015.08.027     Document Type: Article

References (39)

1. Adelman K., Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 2012, 13:720-731.
2. Bruner K.M., Hosmane N.N., Siliciano R.F. Towards an HIV-1 cure: measuring the latent reservoir. Trends Microbiol. 2015, 23:192-203.
3. Calvanese V., Chavez L., Laurent T., Ding S., Verdin E. Dual-color HIV reporters trace a population of latently infected cells and enable their purification. Virology 2013, 446:283-292.
4. Dahabieh M.S., Battivelli E., Verdin E. Understanding HIV latency: the road to an HIV cure. Ann. Rev. Med. 2015, 66:407-421.
5. Dahabieh M.S., Ooms M., Simon V., Sadowski I. A doubly fluorescent HIV-1 reporter shows that the majority of integrated HIV-1 is latent shortly after infection. J. Virol. 2013, 87:4716-4727.
6. Ding D., Qu X., Li L., Zhou X., Liu S., Lin S., Wang P., Kong C., Wang X., Liu L., Zhu H. Involvement of histone methyltransferase GLP in HIV-1 latency through catalysis of H3K9 dimethylation. Virology 2013, 440:182-189.
7. Duverger A., Jones J., May J., Bibollet-Ruche F., Wagner F.A., Cron R.Q., Kutsch O. Determinants of the establishment of human immunodeficiency virus type 1 latency. J. Virol. 2009, 83:3078-3093.
8. Feinberg M.B., Baltimore D., Frankel A.D. The role of Tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation. Proc. Natl. Acad. Sci. 1991, 88:4045-4049.
9. Gallastegui E., Millan-Zambrano G., Terme J.M., Chavez S., Jordan A. Chromatin reassembly factors are involved in transcriptional interference promoting HIV latency. J. Virol. 2011, 85:3187-3202.
10. Greger I.H., Demarchi F., Giacca M., Proudfoot N.J. Transcriptional interference perturbs the binding of Sp1 to the HIV-1 promoter. Nuc. Acids Res. 1998, 26:1294-1301.
11. Guth C.A., Sodroski J. Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid. J. Virol. 2014, 88:4612-4623.
12. Han Y., Lassen K., Monie D., Sedaghat A.R., Shimoji S., Liu X., Pierson T.C., Margolick J.B., Siliciano R.F., Siliciano J.D. Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J. Virol. 2004, 78:6122-6133.
13. Hasgall P.A., Hoogewijs D., Faza M.B., Panse V.G., Wenger R.H., Camenisch G. The putative RNA helicase HELZ promotes cell proliferation, translation initiation and ribosomal protein S6 phosphorylation. PLoS one 2011, 6:e22107.
14. Henning M.S., Morham S.G., Goff S.P., Naghavi M.H. PDZD8 is a novel Gag-interacting factor that promotes retroviral infection. J. Virol. 2010, 84:8990-8995.
15. Ikeda T., Shibata J., Yoshimura K., Koito A., Matsushita S. Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy. J. Infect. Dis. 2007, 195:716-725.
16. Jadlowsky J.K., Wong J.Y., Graham A.C., Dobrowolski C., Devor R.L., Adams M.D., Fujinaga K., Karn J. Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol. Cell. Biol. 2014, 34:1911-1928.
17. Jones J., Whitford W., Wagner F., Kutsch O. Optimization of HIV-1 infectivity assays. BioTechniques 2007, 43:589-590.
18. Kaczmarek Michaels K., Natarajan M., Euler Z., Alter G., Viglianti G., Henderson A.J. Blimp-1, an intrinsic factor that represses HIV-1 proviral transcription in memory CD4+ T cells. J. Immunol. 2015, 194:3267-3274.
19. Kao S.Y., Calman A.F., Luciw P.A., Peterlin B.M. Antitermination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 1987, 330:489-493.
20. Kumar A., Kumar Dorairaj S., Prabhakaran V.C., Prakash D.R., Chakraborty S. Identification of genes associated with tumorigenesis of meibomian cell carcinoma by microarray analysis. Genomics 2007, 90:559-566.
21. Laspia M.F., Rice A.P., Mathews M.B. HIV-1 Tat protein increases transcriptional initiation and stabilizes elongation. Cell 1989, 59:283-292.
22. Lenasi T., Contreras X., Peterlin B.M. Transcriptional interference antagonizes proviral gene expression to promote HIV latency. Cell Host Microbe 2008, 4:123-133.
23. Lewinski M.K., Bisgrove D., Shinn P., Chen H., Hoffmann C., Hannenhalli S., Verdin E., Berry C.C., Ecker J.R., Bushman F.D. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J. Virol. 2005, 79:6610-6619.
24. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.
25. Maldarelli F., Wu X., Su L., Simonetti F.R., Shao W., Hill S., Spindler J., Ferris A.L., Mellors J.W., Kearney M.F., Coffin J.M., Hughes S.H. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science 2014, 345:179-183.
26. Marini B., Kertesz-Farkas A., Ali H., Lucic B., Lisek K., Manganaro L., Pongor S., Luzzati R., Recchia A., Mavilio F., Giacca M., Lusic M. Nuclear architecture dictates HIV-1 integration site selection. Nature 2015, 521:227-231.
27. Mbonye U., Karn J. Transcriptional control of HIV latency: cellular signaling pathways, epigenetics, happenstance and the hope for a cure. Virology 2014, 454-455:328-339.
28. Natarajan M., Schiralli Lester G.M., Lee C., Missra A., Wasserman G.A., Steffen M., Gilmour D.S., Henderson A.J. Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription. J. Biol. Chem. 2013, 288:25995-26003.
29. Palmer A.C., Ahlgren-Berg A., Egan J.B., Dodd I.B., Shearwin K.E. Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter. Mol. Cell 2009, 34:545-555.
30. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23:297-305.
31. Rezaei, S.D., Cameron, P.U., 2015. Human Immunodeficiency Virus (HIV)-1 Integration Sites in Viral Latency. Current HIV/AIDS reports 12, pp. 88-96.
32. Schiralli Lester G.M., Henderson A.J. Mechanisms of HIV transcriptional regulation and their contribution to latency. Mol. Biol. Int. 2012, 2012:614120.
33. Shan L., Yang H.C., Rabi S.A., Bravo H.C., Shroff N.S., Irizarry R.A., Zhang H., Margolick J.B., Siliciano J.D., Siliciano R.F. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. J. Virol. 2011, 85:5384-5393.
34. Sherrill-Mix S., Lewinski M.K., Famiglietti M., Bosque A., Malani N., Ocwieja K.E., Berry C.C., Looney D., Shan L., Agosto L.M., Pace M.J., Siliciano R.F., O'Doherty U., Guatelli J., Planelles V., Bushman F.D. HIV latency and integration site placement in five cell-based models. Retrovirology 2013, 10:90.
35. Siliciano R.F., Greene W.C. HIV latency. CSH Perspect. Med. 2011, 1:a007096.
36. Skawran B., Steinemann D., Becker T., Buurman R., Flik J., Wiese B., Flemming P., Kreipe H., Schlegelberger B., Wilkens L. Loss of 13q is associated with genes involved in cell cycle and proliferation in dedifferentiated hepatocellular carcinoma. Mod. Path 2008, 21:1479-1489.
37. Van Lint C., Emiliani S., Verdin E. The expression of a small fraction of cellular genes is changed in response to histone hyperacetylation. Gene Exp. 1996, 5:245-253.
38. Yang W., Ng P., Zhao M., Wong T.K., Yiu S.M., Lau Y.L. Promoter-sharing by different genes in human genome - CPNE1 and RBM12 gene pair as an example. BMC Genomics 2008, 9:456.
39. Zhang Z., Klatt A., Gilmour D.S., Henderson A.J. Negative elongation factor NELF represses human immunodeficiency virus transcription by pausing the RNA polymerase II complex. J. Biol. Chem. 2007, 282:16981-16988.